Assuming that this is true (you still have not provided any cites) we can explain it one of two ways.
The first would be to assume it to be unintentional. We can consider the incredible amount of chaos on that day, the fact that nobody knew what was going on, how many planes were hijacked or what they were doing. We can consider that having transponders turned off does make it much harder to track a plane, since it goes from a labeled marker on the ATC screen to an unlabeled dot that looks just like all the other dots. We can keep in mind that the government is not one giant telepathic group-mind, and that information doesn’t reliably and instantly pass from one part of it to another, especially when there are no pre-established channels of communication set up. We can also keep in mind that at the time there was no established procedure for sending fighters to intercept a hijacked plane within the borders of the US, as at the time military defense was focused on threats coming from external airspace. We can also keep in mind that the pilots of the fighter planes are not telepathic, and need to be told where to go and what plane to intercept, and this won’t happen even the moment someone realizes that the hijackers are deliberately crashing planes.
The other alternative would be to assume it was intentional. This requires us to assume that the jet fighters would have been sent to intercept the hijacked planes on time, despite there being no procedure and no precedent for this, but they were prevented from doing so by orders issued by some conspiracy. No evidence of said orders has ever surfaces, so we must assume they were covered up with 100% reliability.
The first explanation requires us to assume people are fallible, and that the government is inefficient and does not respond well to sudden, unexpected, chaotic events.
The second explanation requires us to assume that it is possible for conspiracies of people to form that can orchestrate vast and sinister events with not a single person in the conspiracy deciding to release reliable, verifiable evidence of the conspiracy. It requires coverups to be possible and 100% successful, even a decade after the event.
Personally, I find the first explanation far more in line with my experience of how people and governments behave.
I suppose that’s part of the answer to the question in the OP, however. Conspiracy theorists seem to have no problem believing that large numbers of people will all decide to work together to do something like fake 9/11, that not one member of the conspiracy will decide to betray them, and that furthermore the conspiracy can perfectly arrange things so that not one part of their elaborately complex plan can fail. Once you have decided that a conspiracy like this is at work, any unexpected event - like a fighter plane being sent in the wrong direction - can’t have been a mistake, but MUST therefore be part of the conspiracy’s plan.